from ._advmoves import WaltonAdvMove
from ._art import WaltonArt
from ._base import WaltonBase
from ._movements import WaltonMove
from ._polygon import WaltonPolygon
[docs]
class Walton(WaltonAdvMove, WaltonArt, WaltonPolygon):
"""
This is a diagnostic/demo class.
It superposes molecules for merging to test a hypothesis.
In the Frankenstein novel,
(Captain Walton is told the story of the creation of Adam by Victor Frankenstein.
Basically he is just a spectator but actually allows the story to be known:
this class does nothing bar demonstrate what can be done)
Given a list of mols (or smiles as named arguments via the ``from_smiles`` classmethod),
It superposes them via the ``superpose_by_mcs`` or ``superpose_by_map`` methods.
Calling the instance, will merge molecules and yield the merged molecule.
The initial molecules are stored as a list in the attribute ``mols``.
The merged molecule is stored in the attribute ``merged``.
Walton has some methods to speed up operations
.. code-block:: python
demo = Walton.from_smiles(spiropentadiene='C1=CC21C=C2')
demo.ring_on_plane(mol_idx=0, ring_idx=1)
demo.print_coords(mol_idx=0)
Walton is aimed at making life easier to set up an artificial merger condition and show it.
.. code-block:: python
demo = Walton.from_smiles(resorcinol='c1ccc(O)cc1O', eugenol='Oc1ccc(cc1OC)CC=C') # create instance
demo.superpose_by_map({(0,1):{4:0, 3:1, 2:2}}) # superpose molecules by atom indices
demo() # merge (Fragmenstein's Monster)
demo.show() # show 2d, names and 3d
The latter is equivalent to:
.. code-block:: python
display(demo)
demo.to_nglview()
The key feature of the class is that it allows easy transformations
.. code-block:: python
demo = Walton.from_smiles(furan='c1ccco1')
display(demo) # find atom numbers w/o counting
demo.ring_on_plane(mol_idx=0) # flat on xy
demo.atom_on_axis(mol_idx=0, atom_idx=4, axis='x') # ox on axis
# the atom_idx can be actually be passed a Geometry.Point3D:
demo.atom_on_axis(mol_idx=0,
atom_idx=demo.get_centroid_of_atoms(1, 2, mol_idx=0),
axis='x')
"""